I am trying to parse a gctx project using the cmapPy functions but I keep getting the following error:
`---------------------------------------------------------------------------
UnicodeDecodeError Traceback (most recent call last)
in <cell line: 4>()
2
3 # Parse the GCT file
----> 4 gct_data = parse(gct_file_path, convert_neg_666=True)
2 frames
/usr/local/lib/python3.10/dist-packages/cmapPy/pandasGEXpress/parse_gctx.py in parse_metadata_df(dim, meta_group, convert_neg_666)
258 # convert all values to str in temp_array so that
259 # to_numeric works consistently with gct and gct_x parser
--> 260 temp_array = temp_array.astype('str')
261 header_values[str(k)] = temp_array
262 array_index = array_index + 1
UnicodeDecodeError: 'ascii' codec can't decode byte 0xb5 in position 3: ordinal not in range(128)`
I am running this on Google Colab. The parser is running into an issue with decoding and I am wondering if this is because Google Colab runs on python 3 and not python 2.7.11. However, other functions such as the API client, which is also part of cmapPy worked well so it seemed like compatibility wasn't the issue. If someone could take a look at this soon I would appreciate it.
I am trying to parse a gctx project using the cmapPy functions but I keep getting the following error:
`---------------------------------------------------------------------------
UnicodeDecodeError Traceback (most recent call last)
in <cell line: 4>()
2
3 # Parse the GCT file
----> 4 gct_data = parse(gct_file_path, convert_neg_666=True)
2 frames
/usr/local/lib/python3.10/dist-packages/cmapPy/pandasGEXpress/parse_gctx.py in parse_metadata_df(dim, meta_group, convert_neg_666)
258 # convert all values to str in temp_array so that
259 # to_numeric works consistently with gct and gct_x parser
--> 260 temp_array = temp_array.astype('str')
261 header_values[str(k)] = temp_array
262 array_index = array_index + 1
UnicodeDecodeError: 'ascii' codec can't decode byte 0xb5 in position 3: ordinal not in range(128)`
I am running this on Google Colab. The parser is running into an issue with decoding and I am wondering if this is because Google Colab runs on python 3 and not python 2.7.11. However, other functions such as the API client, which is also part of cmapPy worked well so it seemed like compatibility wasn't the issue. If someone could take a look at this soon I would appreciate it.